Hi Ms. Meng, Thank you again for the help! My research head and I had one more question, we opened the structure and visualized the sequence and we want to delete from 90-124 to match up our sequences of our protein. I attached an image of what we are trying to cut out. Thank you again! Rayna DeChance Western New England University Student ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, November 6, 2020 2:51:14 PM To: Rayna L. DeChance Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] help The External Email below originated from outside the University. Unless you recognize the sender, do not click links, open attachments, or respond. Hi Rayna, In the Save PDB dialog (menu: File... Save PDB), there are options to "Save only displayed atoms" or "Save only selected atoms." First show all the atoms, so you can actually see what is there, e.g. menu: Presets... Interactive 1 (all atoms). Then either select the ones you want or hide the ones you don't want. Then in the Save PDB dialog turn on the appropriate option. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> You can select with the mouse (Ctrl-click/drag) or with the "select" command. In the command you can specify model number, ranges of residue numbers, etc., for example: select #3:45-83,90-98 <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> Alternatively you can just delete all the atoms you don't want before you save the file, e.g. with the "delete" command. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Nov 6, 2020, at 11:58 AM, Rayna L. DeChance <rayna.dechance@wne.edu> wrote:

Hi, I was wondering if you knew how to cut out (clip) a part of the protein and save the remaining part as a PDB file. I attached the file I was working with that has the two proteins that are aligned together and we want only a certain part of this alignment to be clip. Thank you <session 1.py>

Hi Rayna, Actually, the red box around the first 30 positions in the sequence probably means that the 3D structure does not include those residues (90-119) anyway. Same thing for the red box around the last 6 positions. First you need figure out what residues are actually in your 3D structure, e.g. by putting the mouse over the termini in the 3D window and seeing what residue number the structure starts and ends with. Then figure out what residues you actually need to delete, and then use one of the methods in my previous answers. Elaine

On Nov 13, 2020, at 2:57 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Rayna, This seems like the same question you already asked. One of the possibilities I gave you was to use the delete command, e.g.

delete :90-124

...if the numbering in the structure is the same as what you showed in the sequence window.

OR, you could use the mouse to drag a box in the sequence window, which will select on the structure, and then you could use command:

delete sel

You might want to try some of the tutorials if you want to become familiar with Chimera:

<https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Nov 13, 2020, at 12:56 PM, Rayna L. DeChance <rayna.dechance@wne.edu> wrote:

Hi Ms. Meng, Thank you again for the help! My research head and I had one more question, we opened the structure and visualized the sequence and we want to delete from 90-124 to match up our sequences of our protein. I attached an image of what we are trying to cut out. Thank you again! Rayna DeChance Western New England University Student From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, November 6, 2020 2:51:14 PM To: Rayna L. DeChance Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] help

The External Email below originated from outside the University. Unless you recognize the sender, do not click links, open attachments, or respond.

Hi Rayna, In the Save PDB dialog (menu: File... Save PDB), there are options to "Save only displayed atoms" or "Save only selected atoms."

First show all the atoms, so you can actually see what is there, e.g. menu: Presets... Interactive 1 (all atoms). Then either select the ones you want or hide the ones you don't want. Then in the Save PDB dialog turn on the appropriate option. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

You can select with the mouse (Ctrl-click/drag) or with the "select" command. In the command you can specify model number, ranges of residue numbers, etc., for example:

select #3:45-83,90-98

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

Alternatively you can just delete all the atoms you don't want before you save the file, e.g. with the "delete" command. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Nov 6, 2020, at 11:58 AM, Rayna L. DeChance <rayna.dechance@wne.edu> wrote:

Hi, I was wondering if you knew how to cut out (clip) a part of the protein and save the remaining part as a PDB file. I attached the file I was working with that has the two proteins that are aligned together and we want only a certain part of this alignment to be clip. Thank you <session 1.py>

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